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RiceLncPedia: a curated knowledgebase of rice Long non-coding RNAs
Summary
Sequence
Coding Potentia
Genome Browser
Expression
Variation
Sequence

>Osa06LNT0340600.1

GGAACAATATGCACAACTGCCGTGCAAAATTATAGCCGCAGACAAATTAAAGCCAGTTGAGCAGTTTTCAGCTCTTTTGGTGCAAGGGGCTTTGTATACATACATAACTTAAAACATAAGATGTAGCTATGCCTGCAACTATGAACTCAGGCATTCAGCCACCTCTCGCACCCGAAATAGCAAAGAATCACGGCACTGAATTTGTAATTCGAAGGCTCAACTAAAGGCCCTGGCTGTGGCTGGGGTCCAGCATCCAAGTCCACCTAAACAAATGTTGCTCTTCTACATACCTCTATGTGGTAGTGAATGGTTAGTCATCGCCGCCACCATCATCAGCCTCCACGGGATCATCATCATACCCTTCATCCTCTTGGTCGCCAGCATCGTCGACATCCATGAGTTCTTGCCCTACAACTGCTTCGTTTATTGCTTCCAATGCTTGCACAGTCCTCAGCTCCGGAGGAGCTCTCTCCACTTTCATGGTTTTCAGCTTATCATCCACAAAGAATGCGGTGAATGGCTTCGGAACCTGGAAATAGCGACCCCGCTCTTTTGCACTCTCAACAAGGTTGTTCCAGTGTTTATCTTCCTTCAATGTTGAAGCAGAACCTACAACTAGTACAGCAGACCTAGCTCTTGTGATGGCGACATTCATTCGTCGAAAATCAGAAACGAACCCAATCTTTTGTTCCTTATTGCACCGAACACATGAGAAAATGACTACTTCCTTTTCACGCCCCTGGAATCCATCAACTGTATTTACGTCTATCACTTCCTTAGACTGATCACCGAAGGTCGACCGAAAATGGTCCTTCAAGAGCTTCACCTGATGCCTGTATGGTGATATGACAGCTACCTGGGAACTAGATTTGAGTTCTGGATAGCGCATAGCCATTTGATGATATAAGAGGGTTATGAATTCCACTTCATCCTCATTCACCCATGAACCACTTCCAGATGGTTGGGACTCAGTCCCATCCACATCAAAGAAGCAGAATGGGCCGAAACAGCTGTAGGAATGCCATGGACGTTTCTTGCTGAGTCCCTCCCCGTCTTCTAGGACACCTTCGTAGAATTCTTTTGAGGGGAATATACTAATCTCTGGGTGCATGCGATACTGAATTTTGAGCATTTGCACAGGAAAACCTGCAGCCTGAAATCTCTTGAATAAACTAGTACCGTACCCTAACTTCTGAGCAGTAGATGAAATTACAGTTGCAGGCAACTGAACTGGGTCACCAACAAGAAAAACTTGTTTGCACCCATGGATCAAGGGTATAAGAGTTGCTGGTTCTACAGCTTGTGCAGCTTCATCAATTATAACAACATCAAAAGCACGAGCCATCCTGCTGAAAATGGATGATCCACTAAAACTTAGCGTAGAAAACACGATGGCTGCTTCATCAAGAATGGAAGATCTAATTCGATCATATTCACCAGCCCCTCGTCTCCCACCATCTGATGAGCGATCCACACCAGAAAGTTTTTGTTGTATAAGGTAATCCATGGAAACTGCTTTAACAGAGTGATGCGCCTTCAGTCCAATTCGCACAATCTTAGGATTATAGGTGTTGTTATTTTCATCGCGTATTCCTGTTTGCAGAACTCGCAGCACAATCTCATCAAGTGCTGAGTTGGATGGAGCACAGACCAAGACATGGGCCCGATACTTGCGATTGGAACTTACGACCTCAGGTTTTAGCTCATTCCCAGTAGGATAAAAACCATCATCGCCGTCAACAGGCATAATTAAATCTCGAGGATTTACACCAATCAGCCACGGGGAGGCCTTCATCCAGTGTGCATGCTTGCCCTCAATATCAAGCTCTGGACCGTGTTTTTTAACATCAAAACCACCTTTGGTTTGCATTCTTGCAGGAGCAGAATGGAGAACAGCACTGAGGAGTCCAAGGATAGTTTGTGTTTTTCCTGTTCCTGGGGGCCCCTGGATAAGAACAAAGGATCTGCGAGAAAGACCTGCGTTGACTGCATCTAGTTGTGAATCATTAAGGTTTGTTTTAAGATAATCCATAAGTGGCTCAGGGACATTCCAAGCACGGTTTTGATCATTCCCACCACTGTTCTTCTCACTAGCTGAAAGAATCAGATCCTTAAAAGGAAGTGATGCTACAGAGTGCATGCCCGAGAATTCTCGCATTATGGTAGACAAGCTGCAAATCTTTAAAATCCAGAGGAAGCTCTCTGTAGTTGAAAAAATGGAAGCAATACGCTGCAGCCTAGAACAGCTCACAGGCTTTGCTACATTAAGATTTTTTATTTCACCTGCCACAAATGTCCTTAGAGAAATCGTTTCTCTGCCACCCCGCTGTTCCACTAAGGCAAAGGCATATGCACTGGGGGTCACTCCCTCTTCAAATTTCTCTTTGGACAGCAGCAGGAGATCGTTCTCCGACACCATCTCCCGGAAATCATCAAGCACGGCCATGGACACCTTGTGGAACCCCTCCGACTCGGTGCACGACGCCACAATCCCCTTCTGCCAGTCCTGCCCAGCCTCTTCCTCCTCGTCGCTGCGCCCCTGGACGATCTGCGCCTTCACCTCCTCGAACAGCAGTGGCTCGAACACAGCGAGGTACTCGGCCACCGAGGCGTACGTGTTCTTCACGCGCCCCAGCCCCTTCGCCTGCTGCTGCCCGCCCTTGGAGTCCGCGACGAGGCGGACGTAGTCCCAGCTGAGGACGATCTTGTGGAAGCGGTCCATGGTGGAGGCGGCGACGCCCGACGAGGAGGAAGAGGCGCCGCCTCCGCCTCCGCCGCCGCCGGATTTGTCCACCGCCATTGGGGCGGCGGCGCGGCGGCGAGAGAAGGGGGTTCTGGGGTTTAGTGAGCCGCCGGCGCTGCAGCGGCAAACAGCCTCGCTCTGTGTGGTGGCCTGGCGGACTGGCGGCCTGCACGCCTGGCCGAGCCCCAACGCCGCACGGCCGCAGCCGTCGACGCGCCGCCTGCACGCCTCGGCGCCTCCTGCCGCCGACGCAGCCGCGCACGCCGCAGCCGGAAGCCTCCGCCGCAGCCGCCGACGAGCACGCTGCAGACTAGACTGCAGTCGCCGCCGCCCGACGCGCCGCCTAGGCTCCTACCCGCCTTGGCGCCGCCTTCCGCCGACGCAGCCGGAAGTCGCCGCCGCCGCACTGCCGCACGTCCTCGCCGCCACACCGCGCACGTCC

Coding Potentia
Explanation CPC Score
noncoding (weak) -0.5716
Genome Browser
Expression
Variation
Transcript ID Chromosome Locus Ref Alt
Osa06LNT0340600.1 6 11787808 T C
Transposon
Transcript ID Transposon ID Chromosome Strand Start End Counts
small RNA targets
Transcript ID MiRNA ID Inhibition Expectation Score Binding Start Binding End
Osa06LNT0340600.1 osa-miR5534b Cleavage 4.0 15.295 1 21
Osa06LNT0340600.1 osa-miR1440b Cleavage 4.0 11.804 1 21
Osa06LNT0340600.1 osa-miR395c Cleavage 3.5 16.932 1 21
Osa06LNT0340600.1 osa-miR395a Cleavage 3.5 16.932 1 21
Osa06LNT0340600.1 osa-miR395u Cleavage 4.5 16.932 1 21
Osa06LNT0340600.1 osa-miR172c Cleavage 5.0 12.445 1 21
Osa06LNT0340600.1 osa-miR419 Translation 5.0 11.704 1 21
Osa06LNT0340600.1 osa-miR1435 Translation 4.5 15.525 1 20
Osa06LNT0340600.1 osa-miR1861g Translation 4.5 11.82 1 22
Osa06LNT0340600.1 osa-miR2095-3p Translation 4.0 18.879 1 20
Osa06LNT0340600.1 osa-miR2098-5p Cleavage 3.0 11.163 1 20
Osa06LNT0340600.1 osa-miR5502 Translation 4.5 15.947 1 22
Osa06LNT0340600.1 osa-miR5506 Translation 3.5 11.646 1 21
Osa06LNT0340600.1 osa-miR2275c Cleavage 5.0 22.978 1 23
Osa06LNT0340600.1 osa-miR2275c Cleavage 4.5 14.326 1 23
QTL
Transcript ID Chr QTL Gene Character Major Character Minor Marker Interval1 Marker Interval2
Osa06LNT0340600.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0340600.1 6 qPHw6-2 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0340600.1 6 qSFWd6 Resistance or Tolerance Other soil stress tolerance RG424 RZ667
Osa06LNT0340600.1 6 qSPN-6 Morphological trait Panicle/flower C235 G294
Osa06LNT0340600.1 6 gw-6 Morphological trait Seed C235 G294
Osa06LNT0340600.1 6 ph6 Morphological trait Dwarf RZ667 RG653
Osa06LNT0340600.1 6 qLDLJ-6-1,2,3 Physiological trait Source activity RM217 RM3
Osa06LNT0340600.1 6 qNFGP-6 Physiological trait Source activity RM136 RG456
Osa06LNT0340600.1 6 qSF-6 Physiological trait Source activity RM136 RG456
Osa06LNT0340600.1 6 gp6 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0340600.1 6 qRS6-1 Morphological trait Shoot/Seedling RZ667 RG424
Osa06LNT0340600.1 6 qGY6-1 Morphological trait Seed RZ667 RG424
Osa06LNT0340600.1 6 qLVBSL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0340600.1 6 qLVBTL6-1 Morphological trait Panicle/flower RZ667 RG424
Osa06LNT0340600.1 6 qSL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0340600.1 6 qTL6-1 Morphological trait Culm/leaf RZ667 RG424
Osa06LNT0340600.1 6 nan Physiological trait Eating quality RM253 RM162
Osa06LNT0340600.1 6 qHD-6-1 Physiological trait Flowering RG424 RZ667
Osa06LNT0340600.1 6 qPH2-6-1 Morphological trait Dwarf RG424 RZ667
Osa06LNT0340600.1 6 qTN2-6-1 Morphological trait Culm/leaf RG424 RZ667
Osa06LNT0340600.1 6 amy6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0340600.1 6 asv6-1 Physiological trait Eating quality RM3 RM217
Osa06LNT0340600.1 6 tgw6.1 Physiological trait Source activity RG264 RM3
pre-miRNA
Transcript ID Pre-miRNA Identity(%) Alignment Length Pre-miRNA start Pre-miRNA end E-value Bitscore
GWAS
Transcript ID Chromosome Locus Trait Value Plus Minus